@numchapentry{Introduction}{1}{Introduction}{1}
@numsecentry{General Overview}{1.1}{General Overview}{1}
@numsubsecentry{What is MetaQTL}{1.1.1}{What is MetaQTL}{1}
@numsubsecentry{Definition of the Problem}{1.1.2}{Definition of the Problem}{1}
@numsecentry{Citing MetaQTL}{1.2}{Citing MetaQTL}{2}
@numsecentry{How to Get and Install MetaQTL}{1.3}{How to Get and Install MetaQTL}{2}
@numsecentry{Getting Help}{1.4}{Getting Help}{2}
@numsecentry{General Usage of the Programs}{1.5}{General Usage of the Programs}{2}
@numsecentry{References}{1.6}{References}{2}
@numchapentry{Data Base}{2}{Data Base}{4}
@numsecentry{Overview}{2.1}{Overview}{4}
@numsubsecentry{Experiment Table}{2.1.1}{Experiment Table}{4}
@numsubsecentry{Trait Ontology Table}{2.1.2}{Trait Ontology Table}{5}
@numsubsecentry{GLMdb}{2.1.3}{GLMdb}{5}
@numsubsecentry{QTLdb}{2.1.4}{QTLdb}{6}
@numsecentry{MetaDB}{2.2}{MetaDB}{6}
@numsubsecentry{Command Line Options}{2.2.1}{}{6}
@numchapentry{Meta Analysis}{3}{Meta Analysis}{8}
@numsecentry{Consensus map}{3.1}{Consensus map}{8}
@numsubsecentry{InfoMap}{3.1.1}{}{8}
@numsubsubsecentry{Method}{3.1.1.1}{}{8}
@numsubsubsecentry{Command Line Options}{3.1.1.2}{}{8}
@numsubsubsecentry{Output}{3.1.1.3}{}{9}
@numsubsecentry{ConsMap}{3.1.2}{}{10}
@numsubsubsecentry{Method}{3.1.2.1}{}{10}
@numsubsubsecentry{Command Line Options}{3.1.2.2}{}{10}
@numsubsecentry{Output}{3.1.3}{}{11}
@numsecentry{QTL Projection}{3.2}{QTL Projection}{11}
@numsubsecentry{Method}{3.2.1}{}{11}
@numsubsecentry{QTLProj}{3.2.2}{}{12}
@numsubsubsecentry{Command Line Options}{3.2.2.1}{}{12}
@numsubsubsecentry{Output files}{3.2.2.2}{}{12}
@numsecentry{QTL Clustering}{3.3}{QTL Clustering}{13}
@numsubsecentry{ClustQTL}{3.3.1}{}{13}
@numsubsubsecentry{Method}{3.3.1.1}{}{13}
@numsubsubsecentry{Command Line Options}{3.3.1.2}{}{13}
@numsubsubsecentry{Output}{3.3.1.3}{}{13}
@numsubsecentry{QTLTree}{3.3.2}{}{15}
@numsubsubsecentry{Method}{3.3.2.1}{}{15}
@numsubsubsecentry{Command Line Options}{3.3.2.2}{}{16}
@numsubsubsecentry{Output}{3.3.2.3}{}{16}
@numchapentry{Visualization}{4}{Visualization}{18}
@numsecentry{MapView}{4.1}{MapView}{18}
@numsubsecentry{Command Line Options}{4.1.1}{}{18}
@numsubsecentry{Drawing Parameters}{4.1.2}{}{18}
@numsecentry{MMapView}{4.2}{MMapView}{21}
@numsubsecentry{Command Line Options}{4.2.1}{}{21}
@numsubsecentry{Drawing parameters}{4.2.2}{}{22}
@numsecentry{MQTLView}{4.3}{MQTLView}{25}
@numsubsecentry{Command Line Options}{4.3.1}{}{25}
@numchapentry{Utilities}{5}{Utilities}{31}
@numsecentry{A2Xml}{5.1}{A2Xml}{31}
@numsubsecentry{Command Line Options}{5.1.1}{}{31}
@numsecentry{Xml2A}{5.2}{Xml2A}{33}
@numsubsecentry{Command Line Options}{5.2.1}{}{33}
@numsecentry{QTLClustInfo}{5.3}{QTLClustInfo}{33}
@numsubsecentry{Command Line Options}{5.3.1}{}{33}
@numsecentry{QTLModel}{5.4}{QTLModel}{34}
@numsubsecentry{Command Line Options}{5.4.1}{}{34}
@numsecentry{References}{5.5}{Utilities-References}{35}
@numchapentry{Tutorial}{6}{Tutorial}{36}
@numsecentry{Tutorial Introduction}{6.1}{Tutorial Introduction}{36}
@numsecentry{Step 1 - Creating the XML Database}{6.2}{Step 1 - Creating the XML Database}{36}
@numsecentry{Step 2 - Building the consensus map}{6.3}{Step 2 - Building the consensus map}{36}
@numsubsecentry{Checking chromosome connection and marker order consistency}{6.3.1}{}{36}
@numsubsecentry{Building the consensus map}{6.3.2}{}{41}
@numsecentry{Step 3 - Projection of the QTL}{6.4}{Step 3 - Projection of the QTL}{45}
@numsecentry{Step 4 - QTL Clustering}{6.5}{Step 4 - QTL Clustering}{47}
@numsubsecentry{QTL Clustering}{6.5.1}{}{47}
@numsubsecentry{QTL Tree}{6.5.2}{}{50}
@numsecentry{Step 4 - Post processing}{6.6}{Step 5 - Post processing}{52}
@numsubsecentry{Extracting the meta-QTL}{6.6.1}{}{52}
@numsubsecentry{Projection of the meta-QTL}{6.6.2}{}{52}
@appentry{Copying This Manual}{A}{Copying This Manual}{54}
@unnsecentry{ADDENDUM: How to use this License for your documents}{10000.1}{}{60}
